Analysis of activity space by fragment fingerprints, 2D descriptors, and multitarget dependent transformation of 2D descriptors

Journal of Chemical Information and Modeling

Volumn 46, Issue 3, 2006, Pages 1078-1083

  Givehchi, Alireza ^a,b   Bender, Andreas ^c,d   Glen, Robert C ^c  

^a GOETHE UNIVERSITY   (Germany)

^b UNIVERSITY HOSPITAL MÜNSTER   (Germany)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); DECISION THEORY; NEURAL NETWORKS; TREES (MATHEMATICS); TWO DIMENSIONAL;

MOE AND FRAGMENT-BASED DESCRIPTORS (MOLPRINT 2D); PHYSICOCHEMICAL DESCRIPTOR VECTORS; PLATELET ACTIVATING FACTOR ANTAGONISTS; REDUCTASE INHIBITORS;

ENZYME INHIBITION;

DIPEPTIDYL CARBOXYPEPTIDASE INHIBITOR; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; SEROTONIN RECEPTOR AFFECTING AGENT; THROMBOCYTE ACTIVATING FACTOR; THROMBOXANE A2;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHEMISTRY; DRUG ANTAGONISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ANGIOTENSIN-CONVERTING ENZYME INHIBITORS; HYDROXYMETHYLGLUTARYL-COA REDUCTASE INHIBITORS; NEURAL NETWORKS (COMPUTER); PLATELET ACTIVATING FACTOR; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SEROTONIN AGENTS; THROMBOXANE A2;

EID: 33745347762     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0500233     Document Type: Article

References (32)

1. Virtual screening for bioactive molecules; Böhm, H. J., Schneider, G., Eds.; Wiley-VCH: Weinheim, 2000.
2. Kubinyi, H. In Computer-assisted lead finding and optimization - Current tools for medicinal chemistry; van de Waterbeemt, H., Testa, B., Folkers, G., Eds.; Wiley-VCH: Weinheim, 1997; pp 9-28.
3. Johnson, M. A.; Maggiora, G. M. Concepts and Applications of Molecular Similarity; John Wiley & Sons: New York, 1990.
4. Bender, A.; Glen, R. C. Molecular Similarity: A Key Technique in Molecular Informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
5. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
6. Sheridan, R. P.; Feuston, B. P.; Mairov, V. N.; Kearsley, S. K. Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR. J. Chem. Inf. Comput. Sci. 2004, 44, 1912-1928.
7. Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Wold, S. Introduction to multi- and megavariate data analysis using projection methods (PCA & PLS); Umeå: Umetrics, 1999.
8. Noonan, R. D.; Wold, H. Partial least squares. In Educational Research, Methodology, and Measurement: An International Handbook; Reeves, J. P., Ed.; Pergamon Press: Oxford, 1988; pp 710-716.
9. Geladi, P.; Kowalski, B. R. Partial Least-Squares Regression: A Tutorial. Anal. Chim. Act. 1986, 185, 1-17.
10. Helland, I. S., On the structure of partial least squares. Commun. Statistic - Simul. 1988, 17, 1581-607.
11. Givehchi, A.; Dietrich, A.; Wrede, P.; Schneider, G., ChemSpace-Shuttle: A tool for data mining in drug discovery by classification, projection, and 3D visualization. QSAR Comb. Sci. 2003, 5, 549-559.
12. Quinlan, J. R. Induction of Decision Trees. Mach. Learning 1986, 1, 81-106.
13. Glen, R. C.; A-Razzak, M. Applications of Rule-Induction in the Derivation of quantitative structure -activity relationships. J. Comput.-Aided Mol. Des. 1992, 6, 349-383.
14. Zupan, J.; Gasteiger, J. Neural Networks in Chemistry and Drug Design. An Introduction; Wiley-VCH: Weinheim, 1999.
15. Sadowski, J. Database Profiling by Neural Networks. In Virtual screening for bioactive molecules; Böhm, H.-J., Schneider, G., Eds.; Wiley-VCH: Weinheim, 2000; pp 117-130.
16. Schneider, G.; Wrede, P. Artificial neural networks for computer-based molecular design. Prog. Biophys. Mol. Biol. 1998, 70, 175-222.
17. Schneider, G.; Nettekoven, M. Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using self-organizing maps. J. Comb. Chem. 2003, 5, 233-237.
18. Goldberg, D. E. Genetic Algorithms in search, Optimization and Machine Learning; Addison-Wesley: MA, 1989.
19. Schneider, G. Evolutionary Molecular Design in Virtual Fitnet Landscape. In Virtual screening for bioactive molecules; Böhm, H. J., Schneider, G., Eds.; Wiley-VCH: Weinheim, 2000; pp 161-186.
20. Weber, L. Practical Approaches to Evolutionary Design. In Virtual screening for bioactive molecules; Böhm, H. J., Schneider, G., Eds.; Wiley-VCH: Weinheim, 2000; pp 187-205.
21. Givehchi, A.; Schneider, G. Impact of descriptor vector scaling on the classification of drugs and nondrugs with artificial neural networks. J. Mol. Model. 2004, 10, 204-211.
22. Givehchi, A.; Schneider, G. Multi-space classification for predicting GPCR-ligands. Mol. Div. 2005, 9(4), 371-83.
23. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular similarity searching using atom environments, information-based feature selection, and a naive Bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178.
24. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors: evaluation of performance. J. Chem. Inf. Comput. Sci. 2004, 44, 1708-1718.
25. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors; WILEY-VCH: Weinheim, 2000.
26. Morphy, R.; Kay, C.; Rankovic, Z. From magic bullets to designed multiple ligands. Drug Discovery Today 2004, 9, 641-651.
27. Sheridan, R. P. J. Finding multiactivity substructures by mining databases of drug-like compounds. Chem. Inf. Comput. Sci. 2003, 43, 1037-1050.
28. Briem, H.; Lessel, U. F. In vitro and in silico affinity fingerprints: Finding similarities beyond structural classes. Perspect. Drug Discovery Des. 2000, 20, 231-244.
29. Chemical Computing Group Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Quebec, Canada H3A 2R7, http://www.chemcomp.com.
30. (30) The R Project for Statistical Computing, http://www.r-project.org/.
31. Witten, I. H.; Frank, E. Data Mining: Practical machine learning tools with Java implementations; Morgan Kaufman: San Franciso, CA, 2000.
32. Clark, M.; Cramer, R. D.; Vanopdenbosch, N. Validation of the General-Purpose Tripos 5.2 Force-Field. J. Comput. Chem. 1989, 10, 982-1012.